The polymerase chain reaction, cloning, and other amplification methods have been the cornerstones of genetic analysis. Technologies that are deriving from these methods have led to the genomics revolution that we see today. The sequencing of the human genome published in 2001 has been made possible because of the ability to clone and amplify DNA. Likewise, there are many other methods of analyzing DNA that are dependent on these technologies.
Single molecule detection, as defined in this application, is the detection of one fluorophore or one molecule. Single molecule detection has only been recently possible through the use of advanced optical detection methods. These methods include CCD fluorescence detection such as by Sase et al., 1995. Other methods that have achieved single molecule sensitivity include fluorescence correlation spectroscopy (Eigen and Rigler, 1994; Kinjo and Rigler, 1995), far-field confocal microscopy (Nie et al., 1994), cryogenic fluorescence spectroscopy (Kartha et al., 19995), single molecule photon burst counting (Haab and Mathies, 1995; Castro and Shera, 1995), two-photon excited fluorescence (Mertz, 1995), and electrochemical detection (Fan and Bard, 1995). These methods have not been applied extensively to the study of genetics because of difficulty in their implementation. Accordingly, most of these detection methodologies have not gained the attention of geneticists and molecular biologists.